Nuclear magnetic resonance study of hydrogen-bonded ring protons in oligonucleotide helices involving classical and nonclassical base pairs

Abstract

A study of the exchangeable ring nitrogen protons in aqueous solutions of oligonucleotide complexes involving Watson-Crick base pairs as well as Hoogsteen pairs and other nonclassical hydrogen bonding schemes shows that resolvable resonances in the low-field (-10 to -16 ppm from sodium 4,4-dimethyl-4-silapentanesulfonate) region can be detected in a variety of structures other than double stranded helices. Ring nitrogen proton resonances arising from the following hydrogen-bonding situations are reported: (1) AT and GC Watson-Crick base pairs in a self-complementary octanucleotide, dApApApGpCpTpTpT; (2) U-A-U base triples in complexes between oligo-U15 and AMP; (3) C-G-C+ base triples in complexes between oligo-C17 and GMP at acid pH; (4) s4U-A-s4U base triples in complexes between oligo-s4U15 and AMP, all of which involve both Watson-Crick and Hoogsteen base pairing to form triplexes; (5) C-C+ base pairing between protonated and unprotonated C residues in oligo-C17 at acid pH; and (6) I4 base quadruples in the four strand association among oligo-I at high salt. The behavior of the dA3G-CT3 helix is consistent with both fraying of the terminal base pairs and presence of intermediate states as the helix opens. In the monomer-oligomer complexes, under the conditions used here, the exchange appears to be governed by the dissociation rate of monomer from the complex. These findings suggest that those tertiary structure hydrogen bonds in tRNA involving ring nitrogen protons should have representative resonances in the low-field (11-16 ppm) proton NMR region in H2O.

A historical account of hoogsteen base‐pairs in duplex DNA

“…The only real experimental indication that both G-C and A-T/U could form WC base-pairs in double and triple helices came from subsequent solution NMR studies of tRNA and polynucleotide complexes in 1970s. 19,22–27 These studies, which were performed under physiological solution conditions in the absence of potentially perturbing crystal packing forces, showed distinct chemical shift signatures that were consistent with theoretical predictions for WC rather than HG hydrogen bonding in A-T/U base-pairs.…”

“…17 G-C + HG base-pair were subsequently used to explain how poly(rC) associates with poly(dC)-poly(dG) duplexes to form triplexes under acidic conditions 18 and NMR studies provided chemical shift evidence for protonated G-C + HG base-pairs at cytosine N3 in a poly(dC)-poly(dC) complex with dGMP at low pH. 19 The first crystallographic observation of G-C + HG base-pair came many years later for a DNA duplex bound to the bisintercalating antibiotic triostin A. 20 …”

Biological Magnetic Resonance

“…The resonance at 13.8 ppm, one of the sharpest features in the E. coli tRNA mixed spectrum (Bolton and Kearns, 1975) is assigned to Ass' T 54, and this assignment is consistent with recent studies of A . U 2 (Kallenbach et al, 1976). Robillard et al (1976) assign a resonance at 14.3-14.1 of several tRNAs to the Ass' T 54 base pair, but this assignment is eliminated by experiments discussed later in this paper and elsewhere (Jones et aI., 1977).…”

Probing the Potential Role of Non-B DNA Structures at Yeast Meiosis-Specific DNA Double-Strand Breaks

“…4 iA shows the 14.5-16.5 ppm motif of the 1 H NMR spectrum at 27 C of 24-mer C-rich ssDNA recorded on an 800-MHz spectrometer. The spectrum shows peaks between 14.8 and 16.1 ppm, which is a characteristic feature of C-C þ pairing via protonation of one of the C-residues at the N3 position (97). The DNA sequence, which is rich in C-residues, can pair, either via inter-or intramolecular folding, wherein the C residues come closer to form C-C þ pairs.…”